SLX4IP

SLX4 interacting protein

Basic information

Region (hg38): 20:10435304-10636829

Previous symbols: [ "C20orf94" ]

Links

ENSG00000149346 ∙ NCBI:128710 ∙ OMIM:615958 ∙ HGNC:16225 ∙ Uniprot:Q5VYV7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLX4IP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLX4IP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in SLX4IP

This is a list of pathogenic ClinVar variants found in the SLX4IP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-10556255-G-C		not specified	Uncertain significance (Mar 18, 2024)
20-10556318-G-A		not specified	Uncertain significance (May 02, 2023)
20-10560717-A-G			Likely benign (May 01, 2022)
20-10560773-G-A		not specified	Uncertain significance (Apr 18, 2024)
20-10560803-A-G		not specified	Likely benign (Jan 07, 2022)
20-10601814-G-A		not specified	Uncertain significance (Mar 31, 2024)
20-10621392-C-T		not specified	Uncertain significance (Mar 22, 2023)
20-10622700-C-T		not specified	Uncertain significance (Jun 07, 2023)
20-10622843-A-G		not specified	Uncertain significance (Mar 15, 2024)
20-10622861-G-A		not specified	Uncertain significance (Nov 27, 2023)
20-10622895-C-A		not specified	Uncertain significance (Mar 01, 2023)
20-10623080-A-G		not specified	Uncertain significance (Oct 17, 2023)
20-10623118-A-C		not specified	Uncertain significance (May 18, 2023)
20-10623140-G-T		not specified	Uncertain significance (Dec 07, 2023)
20-10623198-A-G		not specified	Uncertain significance (Nov 01, 2022)
20-10623258-A-G		not specified	Uncertain significance (Oct 30, 2023)
20-10623352-A-C		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLX4IP	protein_coding	protein_coding	ENST00000334534	7	201527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.79e-12	0.0311	125588	1	159	125748	0.000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.327	203	217	0.938	0.0000114	2664
Missense in Polyphen		45	47.129	0.95483		657
Synonymous	0.343	76	79.9	0.951	0.00000438	779
Loss of Function	-0.0277	18	17.9	1.01	9.21e-7	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00218	0.00217
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000278	0.000272
Finnish	0.00331	0.00324
European (Non-Finnish)	0.000270	0.000264
Middle Eastern	0.000278	0.000272
South Asian	0.000360	0.000359
Other	0.000536	0.000489

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=Chromosomal aberrations involving SLX4IP are found in acute lymphoblastic leukemia. A site-specific deletion within the 5' region of SLX4IP is found in 30% of childhood acute lymphoblastic leukemia in general and more than 60% of ETV6/RUNX1- rearranged acute lymphoblastic leukemia. Breakpoints within SLX4IP reveal junctions with typical characteristics of illegitimate V(D)J mediated recombination. SLX4IP deletions are significantly associated with male gender and ETV6/RUNX1-rearranged acute lymphoblastic leukemia. {ECO:0000269|PubMed:24045615}.

Recessive Scores

• pRec: 0.0573

Intolerance Scores

• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.0170
• hipred: N
• hipred_score: 0.147
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slx4ip
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Molecular function: protein binding